Alignments for a candidate for proB in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for proB in Dinoroseobacter shibae DFL-12

Align glutamate 5-kinase (EC 2.7.2.11) (characterized)
to candidate 3608061 Dshi_1467 glutamate 5-kinase (RefSeq)

Query= reanno::Korea:Ga0059261_3512
         (367 letters)



>FitnessBrowser__Dino:3608061
          Length = 368

 Score =  310 bits (794), Expect = 4e-89
 Identities = 189/362 (52%), Positives = 235/362 (64%), Gaps = 10/362 (2%)

Query: 12  LVVKIGSALLVDP-EGAIRRDWLEGIAADIAARVRAGQQIAVVSSGAIALGARRLKLAKG 70
           LVVKIGSALLVD   GA+R+DWL G+A D+A     G  + +VSSG+IALG R L L  G
Sbjct: 10  LVVKIGSALLVDQASGALRQDWLTGLAQDVAEIRARGADVILVSSGSIALGRRVLGLGTG 69

Query: 71  GRASLEDAQAAAATGQIALSQVWAEVLAANGLTAAQMLVTLDDLEDRRRYLNAAATLGRL 130
               LE AQAAAA GQI L++ + EVLA + +T AQ+LVTL+D  DRRRYLN  ATLG L
Sbjct: 70  A-LPLEQAQAAAAVGQIRLARAYEEVLAPHKITTAQVLVTLEDSTDRRRYLNTRATLGTL 128

Query: 131 LSLGVVPVINENDSVATAEIRFGDNDRLAARVAQAADASGVVLLSDIDGLYDRNPAL-PG 189
           LSLGV P++NEND++AT EIR+GDNDRLAA+VA  A A  +VLLSD+DGLY  NPA  P 
Sbjct: 129 LSLGVTPIVNENDTIATDEIRYGDNDRLAAQVAVMAGADQLVLLSDVDGLYTANPATDPT 188

Query: 190 AVHIPVVERIDGRVEGMADRGSASGMGSGGMVSKIEAARIAASAGVSLAIANGRVDRPLS 249
           A     V+ I   +E MA   + SG+  GGM +K+ AAR A  AG ++AI  G   RPL 
Sbjct: 189 ATRFDRVDEITPEIEAMAG-DAVSGLSKGGMKTKLMAARTAMDAGCAMAITEGARPRPLK 247

Query: 250 A---DARHTVFLPE-KRTRARKAWLAGRLTAKGSIIVDAGAAQALTEGRSLLAIGATAIR 305
           A    A  T F+P      ARK W+A  +  +G I VDAGA  AL  G+SLL  G T + 
Sbjct: 248 ALMDGAPATWFVPRTDPLAARKHWIAA-MKPRGEITVDAGACAALKRGKSLLPAGITEVS 306

Query: 306 GMFFRGDLVTIEGPNG-PIARGLSEYDAPDAQAILGTRSDDQGEILGYAPRSTLVHRNHM 364
           G F RGD V I  P+G  + RGL+ Y A +A+AI G RS +   +LGY  R+ L+HR+ M
Sbjct: 307 GAFGRGDPVIILAPDGTALGRGLTRYTAVEARAIRGHRSAEIEAVLGYPGRAVLIHRDDM 366

Query: 365 AL 366
            L
Sbjct: 367 VL 368


Lambda     K      H
   0.319    0.134    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 356
Number of extensions: 21
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 367
Length of database: 368
Length adjustment: 30
Effective length of query: 337
Effective length of database: 338
Effective search space:   113906
Effective search space used:   113906
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 3608061 Dshi_1467 (glutamate 5-kinase (RefSeq))
to HMM TIGR01027 (proB: glutamate 5-kinase (EC 2.7.2.11))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01027.hmm
# target sequence database:        /tmp/gapView.22208.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01027  [M=363]
Accession:   TIGR01027
Description: proB: glutamate 5-kinase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.5e-121  389.8   0.0   7.3e-121  389.6   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608061  Dshi_1467 glutamate 5-kinase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608061  Dshi_1467 glutamate 5-kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.6   0.0  7.3e-121  7.3e-121       3     363 .]      10     368 .]       8     368 .] 0.98

  Alignments for each domain:
  == domain 1  score: 389.6 bits;  conditional E-value: 7.3e-121
                         TIGR01027   3 iVvKlGsssLteesgk.lkrsklaelveqvaklkkaGhevvivsSGavaaGleaLglperpkklaekQalaaVGQgr 78 
                                       +VvK+Gs++L+++ +  l++  l+ l+++va++++ G +v++vsSG++a G + Lgl +    l++ Qa+aaVGQ r
  lcl|FitnessBrowser__Dino:3608061  10 LVVKIGSALLVDQASGaLRQDWLTGLAQDVAEIRARGADVILVSSGSIALGRRVLGLGTGALPLEQAQAAAAVGQIR 86 
                                       8*********9987666************************************************************ PP

                         TIGR01027  79 LmklyeklfsqyglkvaQiLLtradlskrerylNarntleellelgvvpivNENDtvaveeikfGDNDtLsalvaal 155
                                       L ++ye++++ +++++aQ+L t +d ++r+rylN r+tl +ll+lgv pivNENDt+a++ei+ GDND+L+a+va +
  lcl|FitnessBrowser__Dino:3608061  87 LARAYEEVLAPHKITTAQVLVTLEDSTDRRRYLNTRATLGTLLSLGVTPIVNENDTIATDEIRYGDNDRLAAQVAVM 163
                                       ***************************************************************************** PP

                         TIGR01027 156 veAdlLvlltdvdgLydadprtnpdAklieeveeieeelkavagssgssvGTGGmrtKleaaelAsragveviiasg 232
                                        +Ad+Lvll+dvdgLy+a+p t+p+A+++++v+ei+ e++a+ag++ s +  GGm+tKl aa++A++ag  + i++g
  lcl|FitnessBrowser__Dino:3608061 164 AGADQLVLLSDVDGLYTANPATDPTATRFDRVDEITPEIEAMAGDAVSGLSKGGMKTKLMAARTAMDAGCAMAITEG 240
                                       ***************************************************************************** PP

                         TIGR01027 233 ekpekiadlledaavgtlfeakkkklknrkqwilaaseakGkiivdegaeeallekgksLlpagvvevegnFsrgev 309
                                       ++p  + +l+++a+  t f +++  l +rk+wi+a++  +G+i+vd+ga +al++ gksLlpag++ev+g F rg+ 
  lcl|FitnessBrowser__Dino:3608061 241 ARPRPLKALMDGAP-ATWFVPRTDPLAARKHWIAAMKP-RGEITVDAGACAALKR-GKSLLPAGITEVSGAFGRGDP 314
                                       ******99999987.69****************98765.5*************98.********************* PP

                         TIGR01027 310 veilaeegqeigkglvnysseelekikglkseeiedvLgyekkeevvhrdnlvl 363
                                       v ila++g+ +g+gl++y++ e + i g++s+eie+vLgy  +++ +hrd++vl
  lcl|FitnessBrowser__Dino:3608061 315 VIILAPDGTALGRGLTRYTAVEARAIRGHRSAEIEAVLGYPGRAVLIHRDDMVL 368
                                       ****************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (363 nodes)
Target sequences:                          1  (368 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.77
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis